Better This Way
by simplyshelbs16
Summary: Without warning, everything came crashing down. Heartbreak, misunderstandings and a slow burn to making up. Heavy angst.
1. Shattered

Molly silently cried as she packed up whatever things she had left at his flat. Thank God Mrs. Hudson gave her a ring when Sherlock left; she wasn't sure she could face him. It had all happened so suddenly and out of the blue. Nothing prepared her for this. Sherlock Holmes had effectively ended their relationship with no warning signs. One minute, she was happily helping him with an experiment and the next, it might as well have been _her_ heart he was cutting into.

They hadn't been living together yet, but Molly was so sure they were ready to take that step before the ball dropped and crushed her spirit. He wasn't cold to her when he ended it; it was gentle, but it still shook her to her core when his words replayed in her mind. Perhaps his soft demeanor about it is what made it hurt more. She wished he would've been cruel; it would be easier to be angry instead of heartbroken and confused.

With the last of her things packed in the small box, she scurried out of the building and awaited a cab to take her home. It was drizzling and dreary, the chill from the slight breeze making her shiver. An empty cab pulled up and Molly was thankful, never noticing the occupied cab that pulled up behind hers. Sherlock Holmes watched with pain in his heart as a broken Molly left him in the dust. _It's better this way_ , he told himself.

* * *

Weeks passed and Molly hadn't seen Sherlock since he ended them. No more experiments at the lab; not even any cases brought him to the morgue. Her life had done a complete three-sixty and reverted back to the way things were before she first met him. It was boring and uneventful. He had left a gaping hole in her life with no other way to fill it.

"Hey Molls," Greg announced his presence. Her head shot up, hopeful that there was a chance Sherlock would be with him, but there was no sign and her shoulders slumped.

"Hi, what can I help you with?" she asked, unenthusiastically.

"Need to take photos of a Mr. Erickson for a certain git who refuses to leave his flat," he grumbled. Noticing the look on Molly's face at the mention of her still too recent ex, Greg hugged her. "I'm sorry, Molly."

"S'fine," she sniffed. "Thanks, I needed that. Let me roll him out for you."

* * *

Sherlock's wall above the sofa was covered with papers and photographs, string connecting them all. He lifted the photos that Greg had retrieved for him and reached for more string to add them. There wasn't any left. He mumbled to himself in frustration, tearing 221B apart to find something that would work. His grumblings stopped when he came across a small roll of oxford blue yarn that managed to hide beneath his bed. Molly's yarn. He revisited a memory in his mind palace.

 _"Happy Christmas, Sherlock," she smiled gleefully, handing him a gift bag. He lifted the hand-knitted oxford blue scarf out of the plethora of crinkling tissue paper._

 _"Molly, I—thank you so much, sweetheart," he told her, a kiss placed upon her lips. "It's perfect."_

 _"I'm happy you love it," she said, her arms wrapping around him._

 _"Mm, I love you," he spoke softly._

 _"I love you too, Sherlock."_

"Sherlock!" John shouted for the last time, snapping the detective out of his mind palace.

"What? Where's Mary?" he asked.

"She's at home with Rosie," John informed him. "Still not happy with you, by the way."

"It was for the best, John," Sherlock insisted, a lie he kept telling himself.

"Yeah," John laughed in disbelief, "you know, you keep saying that. Who are you trying to convince, Sherlock? Better this way for who, exactly?"

"You're in no position to interrogate me about relationships when you cheated on your wife," Sherlock spat out. "And with my sister no less."

"Fair point, but Mary and I are working through it, not divorcing," he shot back. "I made a mistake and I'm trying to fix it. However, you just gave up altogether, Sherlock. Molly Hooper was your Mary Morstan; still is, and you kicked her to the curb. You're not as clever as you think you are." With that, John stormed out of the flat, leaving Sherlock to huff to himself. He was doing this for Molly; staying away would be better for her, no matter how much pain it would cause him to do so.


	2. Putting Two and Two Together

Another month passed, with no sign of Sherlock. Molly berated herself for desperately wishing he would come flourishing through the morgue's doorway like he used to. She couldn't quite put her finger on it, but the more she replayed their last exchange in her mind, the stranger it seemed to her. She was elbows deep in a cadaver when John Watson burst into the room.

"I don't care what that bloody git says," he muttered to himself before looking up to find Molly in the midst of an autopsy.

"John? Is everything alright? Rosie's okay, right?" she asked.

"Oh, yes, not to worry, but, well, when you're finished here, could you come to this room?" John questioned, slipping a piece of paper with the room number scrawled on it into her lab coat's pocket.

"Sure, but what is it? It's not Mary, is it?" Molly pried with worry.

"He's been asking for you, Molls. Lord knows he doesn't deserve you, but he needs you right now," John told her. He needn't say the name; she knew very well who it was.

"I'll be there as soon as I can," she assured him.

* * *

With bated breath, Molly stepped into the room. Sherlock was unconscious, the heartrate monitor hooked into him. He hadn't shaved in quite some time, leading her to believe he had relapsed the way he did for the Culverton case.

"He's not—"

"High?" John finished. "No, not in the least. I wasn't with him. He's been stabbed and lost quite a bit of blood. He's healing though."

"How long has he been here?" she asked.

"Since last night," he answered. John stood to offer Molly the bedside chair and she gave him a grateful smile before sitting down. "I'll give you a moment." With that, John left for the canteen.

"Sherlock," Molly sighed, hesitantly resting her hand over top his. "What have you gotten yourself into this time?" She brushed her lips against his forehead. Unable to figure out what else to say, Molly began to sing softly to him, a sweet memory replaying in her mind.

 _"Settle down with me; cover me up, cuddle me in…" she sang as she washed up her dishes after the dinner she had with Sherlock at her flat. Molly felt his arms embrace her from behind, humming along to her singing. "Your lips pressed to my neck."_

 _"Mm," he sounded as he trailed kisses over her neck, his nose nuzzling against her every now and then. She lost all ability to focus on singing as she reveled in his affections, leaning into him. Sherlock nibbled at her ear before singing the last chorus to her, his rich baritone reverberating through her._

Molly snapped out of her thoughts and ceased her singing when she felt his hand squeeze hers. He wasn't awake, but he was obviously aware of her presence.

"Miss Hooper," Mycroft Holmes nodded to her.

"Hello, Mycroft, it's been an age," she spoke lightheartedly.

"So it has," he replied, unsure of what to say on his little brother's behalf. Perhaps that was the point, though; it wasn't up to him to clean up this mess. Mycroft had grown to love Molly as a sister, the aftermath of the Sherrinford incident proving she was more than capable of taking care of both Holmes brothers' fragile emotional states.

"I'll, um—I should probably get going. I'm still on the clock," Molly explained, standing up. "It was nice to see you again."

"Likewise, Molly," Mycroft gave a sad smile. It was rare that he ever used her first name, so it still sounded a bit foreign to her. With a small wave, she left for the morgue once more.

* * *

"Hey Molls, is—" John stopped when met with Mycroft's cold eyes.

"You were aware that Miss Hooper was in this room?" the eldest Holmes asked.

"Well, yes, I told her what I knew of what happened," John replied.

"You could have put her at risk by doing that, Doctor Watson," he told him.

"I—no, you know what? Nobody ever tells me a damn bloody thing around here anymore, so how I was I supposed to know!?" John shouted.

"Do not, for my sanity, cause a scene," Mycroft groaned, pinching the bridge of his nose. "Miss Hooper needs to stay far away from my brother until this operation is over; it's better this way." And just like that, the puzzle pieces clicked in John's mind.

"Better this way," he laughed. "Christ, you had something to do with their breakup, didn't you?"

"It wasn't my idea for Sherlock to take that route, if that's what you're implying. I merely suggested she be holed up in a safehouse until it blows over, but no, my brother took it a step too far in my personal opinion," Mycroft ranted.

John knew that whatever operation this was, it was serious and now he was sworn to secrecy. If anyone asked, Sherlock despised Molly. It was only for her safety and she now had three protectors.

* * *

 **Author's Note:** It's all making sense now, isn't it? I wouldn't break them up if I didn't have a good reason, promise.


	3. Epiphany

"Why didn't you tell me?" John asked in frustration. Sherlock was healed, more or less, lounging in his chair after being released from the hospital.

"The less people that know, the better. It has to be believable, John," he explained.

"Okay, but who exactly needs to believe you don't care for Molly?" his best friend inquired.

"It seems there are still associates of Moriarty who weren't exactly part of his web, but they have a vendetta against me. Mycroft received notice that they had planned to go after not only me, but "the girlfriend"," Sherlock explained, using air quotes. "I can't have her in harm's way, especially when it still has Moriarty's name all over it."

"The bloody bastard's dead and he's still managing to get under your skin. Don't you see what's happening, Sherlock? He already won. From beyond the grave, no less," John argued.

"What's done is done, John. All I can do now is ensure her safety," Sherlock sighed. "Do you think it doesn't hurt me too?"

"Well, you could've gone with Mycroft's plan," he pointed out.

"No," Sherlock spoke firmly. "Molly deserves better than to be with someone that will always put her in danger by association."

"Her job alone could put her in danger, Sherlock. She can solve murders by an autopsy," John shot back. "Molly knew what she was getting into by getting involved with you. It was her choice and this should've been her choice too."

"She would've chosen wrong," he replied. With that, John left to go home to his wife and daughter, annoyed with Sherlock's extreme ways of thinking.

* * *

The following weekend, Molly was over at the Watsons' home having tea with Mary and playing with her goddaughter. Rosie was walking now and couldn't get enough of it. She was sitting in her Aunt Molly's lap, flipping through a picture book when the familiar bantering began. A banter session Molly thought she'd never hear again.

"You're too cocky for your own good," John huffed.

"If you would have just listened to me and ducked, we wouldn't even be having this inane conversation," Sherlock's voice sounded with annoyance. Molly held her breath when his eyes met hers for the first time in two months. His heart constricted and his mind entered buffering mode. He searched for gentle ways to convince her to leave. Maybe he should just ignore her? Oh, but he couldn't.

"Mate?" John asked.

"Hmm?" Sherlock finally spoke.

"Well, I should be going," Molly told Mary. "Thanks for today; I needed it." The consulting detective let out a mental sigh of relief that he didn't need to attempt to coerce her to go. Molly placed her hand on his arm affectionately as she passed. "I'm glad you're okay, Sherlock." As she left, his heart ached. _Bless that woman, she still loves me_ , he thought. _I deserve none of it_.

"What have I done?" he finally realized, mentally kicking himself. The pained look in her eyes mixed with the usual loving glance did it for him.

"Do you think this was really the best way now?" Mary asked. Of course, John had told her Sherlock's ridiculous plans.

"No; I've been an utter git," Sherlock admitted.

* * *

Sherlock was searching all over his flat for anything Molly may have left behind out of forgetfulness. He was desperate to have some piece of her other than that ball of yarn. There wasn't a trace of her. Thinking she may have left something in his closet, he searched only to come across a shoebox that definitely wasn't his. It may only be shoes, but it was _something_.

Upon opening it, he saw there were no shoes, but a collection of polaroid photos of them, letters and other keepsakes; all reminders of their relationship. There was a note taped to the inside of the lid written in her hand.

 _My sweet Sherlock,_

 _If you happen to stumble across this, you should know I left it behind on purpose. I have absolutely no idea why you ended things between us, but I think you should have a reminder of how it used to be; a reminder of our love. I never want you to forget our time together or what it felt like to be loved. Even though I don't believe it for a second, if you truly don't love me anymore, I still wanted to say thank you for choosing me, if only for a little while, because I needed it. I needed you. I'll be okay, eventually. I won't say I'm not heartbroken, because I am, but being with you was the single greatest adventure I'll ever have. No matter what, you will always be the love of my life. So, even if you don't want to hear it, I love you. I love you. I love you. Nothing will change that._

 _Take care of yourself, my bumblebee. Love always,_

 _Your honeybee xxx_

Sherlock's eyes filled with tears that only began to fall when he tried to blink them away. There were tear stains on her letter that his now mingled with. His mind was made up…he needed to fix things and fast.

* * *

 **Author's Note:** Thoughts on Molly's gesture? Anyone else crying besides me?


	4. Help From Mummy

_"This was bound to happen, wasn't it?" Molly giggled. She and Sherlock faced one another, still a bit out of breath._

 _"Mm, it was," he muttered, nibbling playfully at her neck. Sherlock pulled her into his arms, her breasts pressed up against his chest. He hugged her tightly to him, never wanting to let go. His hand was buried in her passion-mussed hair. They had just made love for the first time. It had been two months since the events that transpired at Sherrinford and Sherlock felt ready for what was the most emotional experience he had ever had. His Molly was beautiful and fearless with him, giving him her love in every way possible._

 _"Love you," she mumbled against him. Her heart felt as if it might burst. She loved how he held her in such a loving manner, caressing her and running his fingers along her back and in her hair. As Molly nuzzled herself against him, he only hugged her tighter._

 _"I love you too, sweetheart," Sherlock smiled as he brushed his lips against her forehead. They fell asleep quickly, tangled together, to the sound of thrumming heartbeats and calmed breathing._

* * *

Sherlock sat in his chair, the shoebox in his lap. He sorted through the photos, reliving the memories that had been documented. Some of these had been snapped by Greg, John and Mary, he realized as his eyes took in the candids. There was one where he was kissing the tip of Molly's nose in his kitchen. She was baking ginger nuts for him and he had dotted her nose with leftover batter before playfully licking it clean. Her nose was scrunched in the most adorable way.

There were posed photos of them with Rosie and one he had taken whilst they were in bed together. He was snogging her tenderly. Molly hadn't seen it coming as he snapped the photo. It was one of those pictures that were just for them. He found an empty frame and positioned it inside, setting the photo on his bedside table. Sherlock had no idea how he was going to make things up to her once she learned the truth. He had no choice. _Desperate times call for desperate measures_ , he thought as he began to phone his mother.

"Sherlock? Is everything alright? You don't usually call," his mum said. He hadn't told his parents what happened between him and Molly.

"Mummy, I've made a terrible mistake and I don't think there's any chance of redemption," Sherlock's voice broke. He told her everything; what he did, why he did it and asked how he could possibly fix it.

"My dear boy, you need to explain everything to her. I think she'll understand, but you must also realize she's still going to feel hurt. You may have to earn her trust back," his mum told him.

"I've made such a mess of things; I don't see how she'll ever forgive me," his voice trembled with worry.

"Don't overthink it, Sherlock. Use your heart instead of your brain; let it tell you what to do," she said. "I know that's not easy for you, but you must listen to your heart now."

* * *

Molly groaned as she stepped through the hospital doors. The awful lighting causing her eyes to throb with pain from the migraine she woke up with. Her sleep had been awful what with her mind unable to shut down. It was bad enough her thoughts circled around their parting and various nightmares that she hadn't had again until now when Sherlock had first soothed them away.

The hours had dragged on so slowly. Molly was thankful to finally be home after such a long, trying day. She did not, however, look forward to the housework that still had to be done. But as she gave herself a chance to look over her flat, Molly noticed that everything had been done. The dishes were washed, the carpet was vacuumed and a bag of takeaway sat upon her counter.

She emptied the contents of the bag, pulling the food out. Fish and chips with an egg custard tart for dessert, her favourite. At the bottom of the bag, a polaroid photo of her and Sherlock appeared. Her breath caught in her throat as she turned it over to see a short message written on the back.

 _Heard you had a hard day. Take your food and relax in the bath I drew for you. –SH_

Sure enough, as she stepped into the bathroom with her takeaway container, there was a bath ready for her and it was still the perfect warm temperature. He had been here just before she arrived and left, for he was nowhere to be found. All Molly knew, as she relaxed in the bubble-filled water, was that Sherlock Holmes, wherever he was, still loved her.

* * *

 **Author's Note:** He has more more than that planned for Molly, don't worry. Some people may not find it in character, but I personally believe he would go to his mother for this kind of issue. He's absolutely clueless and needed the guidance.


	5. Molly's Discovery

**Thank you to my lovely guest reviewer, Jen, for your kind words! I'm glad it didn't seem OOC lol! Now, who's ready for Molly to find out the truth?**

* * *

"Sherlock? Jesus, what happened to you?" John asked his best friend who stood at his front door, his clothes worse for wear.

"I just need a quick patch up from you is all," Sherlock informed him. "Two of Moriarty's old associates taken into custody, three more to go." John led him inside, closing the door behind them. Mary was awake and alert in the sitting room.

"Sherlock, why do you insist on doing this yourself?" Mary asked. "I had offered my help to you before. I am more than qualified to take them out."

"I should be more than capable of protecting Molly myself," he grumbled.

"Typical male ego," she rolled her eyes. "Honestly, though, should that matter? Whether you like it or not, I will help you capture the last of them. It's better to work together."

"Perhaps I could use your help," Sherlock admitted as John cleaned up his cuts. Some were deep, others just superficial.

"Wise decision, mate," John told him. "I'll help too."

"Then who would take care of Rosamund?" Sherlock questioned. "Mrs. Hudson won't be back until this weekend. Molly has enough on her plate as it is. No, John, you stay with your daughter. There's no need for both of her parents to be put in that situation."

"Unca Lock?" Rosie's small voice drifted through the room, her little feet padding down the hallway. She launched herself into her godfather's open arms. "Bad!" She was scolding him.

"Bad? Why am I bad?" he inquired.

"Aunt Mowwy sad," Rosie told him. Sherlock sighed sadly.

"I know," he replied. "I'll make Aunt Molly happy again, I promise." She seemed satisfied with his answer because she hugged him. As to how he would do that, he was still grasping for a solid idea.

* * *

Molly took a deep breath before knocking on the door.

"Molly, dear, it's been an age!" Mrs. Hudson exclaimed.

"I know," she agreed. "I'm sorry I haven't been by to visit. Is Sherlock in by any chance?"

"He's been gone since yesterday, but I'm sure he'll be back soon," she informed her.

"Could I just have a look around? I'm sure I left something behind," Molly smiled sadly. With a nod from Mrs. Hudson, she climbed up the familiar stairway.

Upon entering 221B, Molly's heart constricted. How was it that it was the same but also different? She looked behind her to see the wall covered in papers and photographs. There were clearly two separate cases being mapped out. With closer inspection, Molly realized one half held only the photos that were in the shoebox she left for him, stringed together with her blue yarn. Her eyes began to fill with tears. Studying the other half of the wall, she noticed Moriarty's name and a short list of other names. _What the hell is going on,_ she asked herself.

"Mister Holmes, if you were half as clever as you think you are, you would do well to stay out of our business," Molly read aloud to herself. "If not, we go after the girlfriend, regardless of how fond Jim was of her. Do I make myself clear?" Everything clicked for her: Sherlock was protecting her by leaving her. "Oh, Sherlock, you ridiculous man."

"Is it really all that ridiculous that I want to keep you safe?" his voice startled her.

"Why didn't you tell me!?" she asked. "It didn't have to be done this way; we could have just pretended to break up. Why would you hurt me like this?" Her tears were falling now and she wiped at them angrily. Molly hated crying in front of him, especially now.

"I—" she was waiting for his answer—"I honestly don't know, Molly. I thought it'd be more believable," Sherlock sighed in defeat. "There is no excuse for what I did. At the time, I thought I was doing right by you. I did it because you deserve better than to be with someone who's association puts you in danger. That's not the kind of life I want for you. You're literally better off without me."

"Sherlock Holmes, don't you dare say that," she cried, jabbing her finger at him. "Has it ever occurred to you that maybe I'd take any kind of life as long as you're in it? It's not up to you to make that decision for me. If given the chance to redo everything, I would still choose you."

"Why?" he asked.

"Oh, I don't know, Sherlock, maybe because I love you more than anything. Maybe it's because you are the most deserving of my love; the most worth man I've ever known. The risk I'm taking to be with you is nothing compared to the pain I felt living a life without you for nearly three bloody months! I am not better off without you, and I can say that for a fact now because you forced me to experience it," Molly told him. The anger was gone from her voice, left only with sadness and disappointment.

"Molly," he reached his hand out to her, his eyes silently asking for permission to touch her. She closed the gap between them, allowing him to envelop her in his arms. Molly inhaled deeply, breathing in his scent that had long ago vanished from his side of her bed and the old dress shirt she had been wearing to sleep in. He lifted her in his arms and carried her over to his chair, setting her in his lap. Her sobs rattled her petite form, causing him to cry with her.

"I'm so sorry," he murmured repeatedly into her hair, rocking her in his arms. "I love you, sweetheart. I am so sorry I hurt you. I'll never forgive myself." Molly felt his tears drop into her hair as he spoke. A mumbled response sounded from her moments later. "What did you say?"

"I said," Molly lifted her head up, her eyes puffy and red, "that I forgive you. But, Sherlock, you're going to have to earn my trust back. Yes, I trust you with my life always, but my heart is a different story."

"I understand," Sherlock told her. They stayed silent for nearly twenty minutes, just holding onto one another, until he spoke again. "May I show you something?" She nodded and slipped off of his lap, adjusting her rumpled clothes. He stood and took her hand, leading her to his bedroom. _If he thinks we're going to make love_ _right now, he's crazy_ , she thought.

"Sherlock, I don't think—" she stopped, realizing what he was showing her. There were differences about the room that weren't there even when they were together. On his bedside table, the photo of them snogging sat on display. A small cat bed was on the floor for Toby and a leather-bound copy of her favourite book, A Tale of Two Cities, sat upon the bedside table she used when she stayed over.

"Open my drawer," he nodded toward his table. Molly furrowed her eyebrows, but did as he said, sitting upon the bed as she opened it. Inside, amongst the mess of notebooks and lab equipment was a single velvet box. She took it in her hands, too nervous to open it.

"This really isn't—"

"I know, Molly. It's not a good time, but that's not why I'm showing it to you," he explained. "I had it an entire month before I made a mess of things. I want you to know that I am serious about you; about us. I realize it's going to take a while for me to earn your trust back and for us to be ready for such a step, so I want you to keep it. If you ever feel like it's the right time, you decide when you want me to properly propose. I am leaving it all up to you."

"You want this kind of future with me?" she asked in surprise. Not for one moment did Molly ever expect him to want marriage.

"Yes, of course I do," Sherlock confirmed.

"Doesn't domestic bliss cause some sort of aneurysm for the Holmes brothers?" she laughed. His mood brightened at the sound of her laughter.

"Maybe for Mycroft," he chuckled. "But I have learned that this is something I do want with you. I have given it plenty of thought." She patted the bed, gesturing for him to sit beside her.

"I will let you know when I think we're ready for that step, okay? I love you, Sherlock, honestly I do, I'm just a bit guarded right now," Molly said softly, her fingers toying with his curls. "Come here." She pressed a tender kiss to his lips.

"Are we going to be okay?" he asked.

"I think so," she smiled.

"And you? Are you okay?" his voice shaken with worry.

"I will be," she answered honestly.

* * *

 **Author's Note:** Things can only get better from here lol! I'm excited to finally be able to start building them back up again. Expect sweet gestures and romance with a sprinkle of danger ;)


	6. Falling In Love Again

Molly woke to the smell of bacon and eggs. As her eyes adjusted, she realized she was still at 221B, in Sherlock's bed no less. _Mrs. Hudson must be cooking in the kitchen_ , she thought as she pulled on Sherlock's blue dressing gown. Not Mrs. Hudson, but Sherlock, was setting the now cleared off kitchen table with breakfast for two.

"Ah, Molly, you're awake," he smiled. _When and how, exactly, did I fall asleep_ , she wondered. It took a moment for her to realize that she had spoken out loud when Sherlock began to answer her. "It was around six in the evening. I believe it was because of two factors: one, I was holding you for quite some time and two, you haven't had a decent night's sleep in at least three months. Sorry about that last one; that was entirely my fault."

"Oh," was all she said as the events from yesterday flooded through her mind. Waking up to Sherlock cooking breakfast had made it feel as if the breakup never even happened, if only for a fleeting moment. He approached her slowly, like he was afraid of scaring her away if he made any sudden movements. Molly realized he was practically tip-toeing around her, not wanting to give her affection if it was unwanted by her. "Sherlock, you don't have to be so scared. You can kiss me; I won't bite." She paused and then added, "Well, sometimes I do," with a giggle, amused by her own joke. This made him relax around her as he pressed a kiss to her cheek.

"Thank you, Molly Hooper," he breathed into her ear.

"For what?" she asked.

"For giving me another chance," he replied. Sherlock knew how fragile their relationship was right now, but yet, it was also the strongest it had ever been. How strange to think that healing together after a rough patch could strengthen them. He was grateful she took him back, for he was sure he would kiss the ground she walked on if she asked.

* * *

The entire day was spent the way Molly wanted to, at Sherlock's insistence. They had stayed in, occasionally paying attention to the crap telly that was put on, but mostly he listened to Molly tell him about how her life was during the last three months; boring workdays, too many double shifts and not enough variety. It was no wonder she hardly ever slept. When she told him that she finally managed to sleep well after he drew that bath for her, he surged with happiness that he had made her life a bit easier.

Sherlock told her of the operation to round up what was left of Moriarty's criminal associates and the night he was caught off guard, resulting in the stab wound in his side that was now a scar.

"I visited you when John told me," Molly admitted. "You weren't awake, obviously, but I was so afraid for you. I sang our song to you; you know, the Ed Sheeran one you sang with me. You squeezed my hand."

"I thought I was dreaming," Sherlock told her. "I didn't know you were actually there at the time. Otherwise, I would've tried harder to wake up." Molly smiled at this. "If it hadn't been for you leaving that shoebox behind, I'm not sure I would have gotten my head out of my arse. The letter you wrote me had me realize how badly I had hurt you. Did you really think I didn't love you anymore?"

"For a while I did tell myself that, but the more I thought about it, the more it didn't make any sense to me," she explained.

"You know I could never stop loving you, right?" Sherlock asked, his voice low. The weight of his words was welcomed in her heart. With her lips slightly parted, he leaned in to capture them with his own. The snogging didn't stop when he pulled away, as he had begun covering her face with affection; her forehead, eyelids, cheeks, nose and jawline, leading down to her neck. All the while, he had one hand in her hair and another placed at the small of her back. His lips traced over the sensitive spot behind her ear, and he nibbled playfully at it just the way she loved. "I will always love you, honeybee."

"I'll always love you too, my bumblebee," Molly spoke softly. She kissed his lips, nuzzling her nose against his all the while.

* * *

"Status report," Mycroft Holmes demanded when Sherlock entered his office.

"Thanks to Mary, we only have one more associate to find and capture," Sherlock spoke proudly.

"And Molly?" the elder Holmes asked.

"Safe…her and Toby are staying with me until all is clear," he informed him.

"The two of you are back together?" Mycroft inquired.

"You needn't ask me that; I'm sure you already worked that bit out yourself," Sherlock replied.

"Good. If you ever pull that again, brother mine, I'm afraid I'll have to interfere," Mycroft told him.

"Then you have nothing to worry about. There's absolutely no chance that it will ever happen again. Nothing could ever convince me to pull a stunt like that a second time," Sherlock explained. "It was the most foolish and idiotic thing I had ever done."

"Second idiotic thing, Sherlock," he pointed out. "I do believe your drug habit takes the number one spot on that list."

"Another item of that list you do not have to worry about, as I did go back to rehab months ago and no longer have a desire to use," he countered.

* * *

Sherlock came home to find it eerily quiet in his flat. Not even Toby had greeted him like usual. Molly had been there an entire week, under his watchful eye for protection, but something felt off. His instincts kicked in, his feet immediately taking him to his bedroom. His throat felt tight and his heart pounded in his chest, silently praying that Molly was safe. Maybe she had gone out and Toby was asleep?

A breath of relief escaped his lips as he found her fast asleep in his bed. Their bed. Toby was curled up against her stomach as she lay on her side. Molly was also curled up much like her beloved cat. He quietly approached her and kissed her forehead, noticing a difference in body temperature. She was fevered. He left the room and returned with a couple of aspirin and a glass of water that he set on her bedside table.

* * *

Molly woke hours later and took the aspirin that Sherlock had left for her. She faintly heard the sound of his violin when she checked the time on her phone. It was nearing three in the morning. Shivering, Molly wrapped Sherlock's dressing gown around her tightly and padded her way into the sitting room. She found him facing the window as he played a most heartbreaking melody.

"Composing?" she asked, her voice hoarse.

"Revising a composition, yes," he elaborated. "What are you doing out of bed? You should be resting."

"I came out to find you," Molly told him. "What's it called? Your composition? It sounds heart-wrenching."

"That is because it is about the most painful time of my life," Sherlock said. "It's called 'Losing the Love of my Life' and in parentheses, 'I'm a git.'"

"Really?" she laughed in disbelief.

"Yes, well, I'll come up with a shorter title eventually. Brevity is the soul of wit and all," Sherlock joked with a flourish of his hand. A giggle escaped her lips at his remark. "Molly, you really should get some more rest."

"It's hard for me to sleep without you," she told him. "Stay with me?"

"Of course, darling," he replied.

* * *

As they lay in bed, with Molly wrapped up in his arms, Sherlock hummed to her softly.

"Molly?"

"Hmm?"

"What can I do?" he asked.

"What do you mean?" she questioned in return.

"What can I do to make you feel better? How do I fix your heart?" Sherlock wondered.

"Oh, Sherlock, you're already doing everything you can," Molly told him. "I'm healing; we both are." She yawned and cuddled in closer when another chill shot through her.

"Goodnight, sweetheart," he whispered to her. Much to Sherlock's surprise, he had fallen asleep not long after she did. They both dreamt of one another that night, filled with past memories and future plans.

* * *

 **Author's Note:** For those of you who expected me to write out the action-packed adventure of taking down Moriarty's associates, I'm sorry, but I am awful at those scenes lol. My main focus of this fic has always been Sherlolly's relationship. Thoughts on the progress they're making?


	7. Loving You Holds Me Together

**Molly soothes away Sherlock's fears once and for all; danger has arisen for both of them. Let's rate this chapter a hard T for slight violence and a classy description of some nighttime loving :p**

* * *

 _"Just make the incision right there," Molly told him. He began to work on the heart she was helping him experiment on. Sherlock had a lot of things weighing heavy on his mind. Would he be willing to risk her life? Would she be safer here with him or would it be better if she stayed away? He knew he would never forgive himself if she were ever put in harm's way. At least there was a better chance of her being able to fall in love with someone else than there was of her surviving the threat that loomed over her._

 _"Molly?" he ceased his experiment._

 _"Hmm?"_

 _"I've been thinking," he began, approaching her slowly, "that maybe we shouldn't do this anymore."_

 _"You mean the experiment?" Molly asked. Sherlock sighed. He knew this wasn't going to be easy for either of them. Could he trust himself to get the words out? Or would he be selfish and abort the entire mission?_

 _"N-no, I'm talking about…us," he managed to get out. "It's better this way." Molly was confused to say the least at his sudden statement. His tone was so gentle as he spoke that cruel word combination._

 _"You don't want me anymore?" her eyes filled with tears. Sherlock's heart broke just as he watched hers break in front of him. He never answered her question, but pressed a kiss to her temple._

 _"Goodbye, Molly Hooper," his voice was shaky, as if he was holding back tears. Molly wanted nothing more than to just run and get lost somewhere. So that's exactly what she did. Her feet ended up taking her to the Watsons' after walking the streets of London for hours in the cold drizzle, tears streaming down her face that could easily be dismissed as droplets of rain._

* * *

Another two weeks had passed and things were improving greatly between them. They fell into a regular routine and were almost back to their version of normal. There was one night that Molly woke around three forty five in the morning to Sherlock calling out for her in his fitful sleep.

"Sherlock," she spoke softly, "darling, wake up, I'm here." His eyes opened slowly, adjusting to her face in the dark. "I'm here." He hugged her tightly to him.

"I'll never let you go again; I don't care how selfish it seems," he told her. "I'm so sorry I hurt you."

"Shhh, it's okay now," Molly assured him. She kissed his forehead, followed by his lips.

"You'll never be alone again," he promised.

"You're so good to me, Sherlock," she told him.

"Am I?" he asked. "I feel like an unworthy arse."

"William Sherlock Scott Holmes, don't you dare start thinking that way," Molly scolded him gently. "You have never been unworthy. Please stop punishing yourself. So, you made a lapse in judgement. You're only human. Your heart was in the right place." She placed her hand over the bare expanse of his chest where his heartbeat accelerated at her touch. "I love you, Sherlock."

Sherlock relaxed in her arms as she kissed him, her tongue slipping between his lips to meet with his. It wasn't long before pajamas were shed and love was being made.

"I missed you," he whispered breathlessly against her lips as he moved with her in slow tandem.

"I missed you too," she sighed in pleasure. "Sherlock…" Tears sprang to her eyes as they reached the pinnacle together. He was kissing her relentlessly; first her lips, then tasting the tears of joy that fell from her brown eyes.

As they lay cuddled close together, Sherlock pressed his lips into her hair and mindlessly traced his fingers over her stomach.

"I love you so much, Molly," he whispered. "My Molly."

"Ask me," was her reply. It didn't process to him at first what she had told him, but he soon understood.

"My darling, Molly, you have always made my heart a better place. You are my home," he confessed. She smiled at him, a twinkle in her eyes. He reached over to her bedside table and retrieved the ring. "I'm not perfect, but I promise to try to be the best husband I can be for you. I promise to always love you. Margaret Elizabeth Hooper, will you marry me?"

"Yes," she answered happily. "Make me your wife, Sherlock. I want to be Molly Holmes." Her words warmed his heart as he slipped the ring on her finger. He brushed his lips over her fingertips and trailed them down to her wrist. They fell asleep eventually, Sherlock's head resting on her breasts with her right hand in his hair, gently twisting his curls. Her newly decorated left hand was laced with his, her ring capturing the glow of the moonlight peering through the window.

* * *

Once Molly had left for work the next morning, Sherlock prepared himself to continue the search for the last remaining threat. At his insistence, Mary was to stay home. It was only one person, after all. He opened his text messages to find one that Molly had sent to him to let him know she was alright.

 **Made it to work in one piece. Don't worry about me. Stay safe, bumblebee. I love you. –M xxx**

His heart swelled with the love he felt for his Molly. He would keep her safe no matter the cost.

* * *

Lunch came quickly, and for that, Molly was thankful. She had three autopsies done and was quite famished by the time she was able to get food in her system.

"Mind if I sit here?" one of the doctors asked. His gray eyes pierced her in a way that made her feel uncomfortable but she didn't deny him a seat at the table, so she nodded, taking a bite of her sandwich.

"Are you new here?" she asked.

"Just started today, yes," he replied. "You're the pathologist here, right? Molly Hooper?"

"You know who I am?" she questioned.

"Yes, well, it's not much of a secret what with you being on the arm of Sherlock Holmes in the papers," he explained. They had both finished eating by now.

"Mm," she sounded. "Well, he's no longer in the picture." Molly began to walk out of the canteen and the man followed. Nothing more was said until he followed her into the morgue.

"Pretty convenient that you two aren't together anymore," he spoke as he shut the door. "Considering your life is in my hands." Molly tried to get around him as he began to close in. She ended up being pushed, the back of her head hitting the edge of the slab. Everything went black.

* * *

"Sherlock," Mycroft's voice on the other end spoke.

"Is this important? I'm undercover," he hissed.

"Look at the headlines online," his brother told him. "There's a man with a gun at St. Bartholomew's." The color drained from Sherlock's face.

"Molly," was all he said before hanging up and catching a cab straight to the hospital. Sherlock hoped he wasn't too late as he tossed a handful of notes at the driver once they reached his destination.

"Sherlo—" Greg began when he saw the consulting detective run towards the entrance.

"Let go of me, I need to get to Molly! Molly!" he shouted. His voice lost its strength as he turned to his friend. "Greg, please." His voice broke. "Please."

"Alright, let him in!" Greg announced. "Bring her back to us, okay? Go, now!" Sherlock didn't waste any time, running into the hospital, taking the elevator down to the bottom floor where the morgue was.

* * *

"Finally woken up, good," the man chuckled.

"You could have killed me already," Molly pointed out.

"I could have, but where's the fun in that if your detective isn't here to see it? Isn't that right, Mr. Holmes?" he sneered.

"Sherlock!" she shouted, happy for the distraction he provided. The man had no escape as Sherlock trapped him to the floor in a fit of rage.

"Molly, get out of here!" he told her. She seemed to disappear from their view. A gun was being held to Sherlock's chest as the man got the upper hand. Suddenly, the gun was kicked out of the man's hand, sliding to the other side of the morgue. With scalpel in hand, Molly dug it into the man's shoulder blade, catching him by surprise, even more so when she shoved him off of Sherlock, who was equally surprised. The culprit had been knocked out by the force of his head hitting the floor from Molly's actions.

"Text Greg," she breathed. "Now."

* * *

"I'm fine," Sherlock insisted as he was being looked over in the ambulance. Molly was being treated, the matted blood in her hair from hitting her head on the slab was cleaned. Luckily, she hadn't needed stitches, but was told to take medication for the pain.

"Hey you," she smiled, sitting beside him, her feet dangling off of the edge of the ambulance. A blanket was being draped around him, which Molly expected him to shove off. "You're in shock?"

"Yes, well, it's not every day you realize how wrong you were and discover that the woman you've been trying to protect can handle herself just fine," Sherlock told her. Molly wrapped her arms around him, pressing a kiss to his cheek.

"I did learn from the best," Molly pointed out. Sherlock furrowed his eyebrows, unable to remember teaching her any of that. He had taught her basic self-defense but she possessed other skills similar to Mary's.

"Mary," it dawned on him.

"And you, well, combined with my anatomical knowledge on where to stick a scalpel," she laughed. "Still think I'm better suited for a different life?"

"No," he replied. "Of course, I wish it didn't have to be this way for you to be with me—"

"But?" she asked.

"But, it is a life you can obviously handle," he finished. "I'm so sorry, Molly."

"It's okay; we're okay," she told him. Their lips met in a passionate kiss…maybe too passionate for the public eye.

"Get a room, you two," Greg laughed.

"Let them be," Anderson glared, secretly happy to have noticed the ring on Molly's finger.

* * *

 **Author's Note:** Went from one type of intensity to another lol! Tell me your favorite parts! There will be an epilogue, so stay tuned!


	8. Epilogue

They had been married for a little over two years now. Rosie was jumping excitedly as her Uncle Sherlock and Aunt Molly constructed an elaborate blanket fort in the sitting room of 221B.

"How do you have so many blankets?" Sherlock chuckled.

"I get cold easily and I like variety," Molly replied with a smile. An image of her unable to resist walking past a display of cosy blankets and throws was conjured up in her mind, causing her to look away guiltily. Sherlock grabbed one of the fleece blankets and wrapped it around Molly's back, pulling her closer to him and taking her by surprise when he began covering her face with playful kisses. Her lighthearted laughter filled the room.

"Uncle Sherlock?" Rosie asked, interrupting her godparents. Sherlock turned to her, encouraging her with a slight raise of his eyebrows. "Thank you for making Aunt Molly happy again." The little girl watched as her Aunt, closely brought to tears, kneeled down to hug her.

The rest of the day was spent in the fort, watching Disney movies on the telly. When John and Mary came to pick up their daughter, Molly was already asleep amongst the blankets that cushioned the floor.

"Molly?" Sherlock asked, poking at her waist. "Sweetheart, wake up." His wife whined slightly before opening her eyes to the view of her husband gazing at her as if she were the most precious thing in the world. "Did you sleep well?"

"Surprisingly, yes," she answered. "I feel much more energized now."

"Well, that's good to hear," he smirked. Molly could hear the implication of his sultry tone.

"Why? Did you have something in mind?" she teased, her index finger tracing his jawline.

"Mm," he sounded at her touch, leaning down to press a kiss to her lips. His fingers were already sliding the straps of her camisole off of her shoulders. Molly gasped as he smoothed his tongue over the pulse point on her neck. "We should make a baby of our own." This was whispered in her ear, his breath hot on her skin.

"Then what are you waiting for?" she asked playfully with a small laugh. "Let's make a baby." Sherlock didn't have to be told twice as he took his wife in his arms. They were going to start a family of their own.

* * *

Molly looked on in awe at her husband as he pressed warm kisses to the slight swell of her belly. She was only just beginning to show. He had just come home from a case, divesting himself of his Belstaff, scarf and jacket, only to greet her with a snogging session right where she lay down on the sofa. Her blouse had risen up to reveal the small baby bump and Sherlock just couldn't contain himself.

"Hello sweetheart," he cooed. "Daddy loves you. And I love your mummy very much." Molly lightly ran her nails over the back of his neck as he rested his head on her belly, nuzzling it affectionately.

"Enjoying yourself?" Molly smiled.

"Very much so," Sherlock replied, his voice sending vibrations through her. "Do you think I'll be any good at this? Being a father?"

"You're already such a wonderful father, Sherlock," she assured him. "Just look at how well you take care of me and our baby."

"Mm," he sounded in agreement. "You've gained three pounds."

"Sherlock!" Molly swatted at him playfully. "Two and a half," she said under her breath. A familiar memory from years ago came to mind for the both of them.

"No, three," he insisted. "But not to worry, my darling, you're carrying our child beautifully."

"So, does domestic bliss suit me, Mister Holmes?" she teased.

"Indeed it does, Mrs. Holmes," he grinned. "I can't wait to meet you, little one."

* * *

Approximately six months later, Molly had given birth to a beautiful baby girl. Sherlock couldn't take his eyes off of her as Molly held her in her arms. Charlotte Mary Margaret Holmes was the name they gave her; Lottie being the nickname she would later be called by. He was in awe as their daughter gripped his pinky in her miniscule hand, dimples indented at each of her knuckles.

"We made her," he mused, tears in his eyes. "We really did that." Molly gave a short laugh, weak from exhaustion.

"Our little girl," she cooed, kissing the top of their daughter's head. In the moment he first laid eyes on her, Sherlock felt the change within him. He would do whatever it took to protect her and to be a good father. His eyes shifted to drink in the image of his wife; sweat matted her hair to her face which was flushed from the exertion of giving birth, her deep brown eyes unmoving from where they focused on Charlotte. A sweet smile graced her lips as she hummed a lullaby quietly.

"You're so beautiful," Sherlock told her, pressing a kiss to her forehead. He rested his head atop Molly's as they both lavished attention onto their daughter. They were both awestruck at the tiny miracle they had created together. They both smiled at the small group of visitors coming through the doorway: Sherlock's parents, Mycroft, John, Mary and Rosie.

"Pretty baby," Rosie smiled. Everyone agreed with the little Watson on that remark. This was their family and they were home.

* * *

 **Author's Note:** thanks for reading, y'all! I'm so happy this story did as well as it did! Until next time!


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